[gmx-users] Error in system_inflate.gro coordinates does not match

[RINU KHATTRI]

hello everyone
i used editconf

editconf -f protein.gro -o protein_newbox.gro -box (membrane box
vectors) -center *x y z*

but in z axis i have been increased box size 10.0000 (previously it is
6.23910   6.17970   6.91950
http://s48.photobucket.com/user/mittukhattri/media/ri_zpsbb51fbd7.png.html?filters[user]=140927090&filters[recent]=1&sort=1&o=0

this is the em.gro first minimization image

 mixing of lipid and protein molecule

kindly help





On Fri, Jul 25, 2014 at 7:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/24/14, 11:57 AM, RINU KHATTRI wrote:
>
>> hello everyone
>> thank you justin
>> i did the same
>> till minimization without the ligand it is in the lipid and center but i
>> edit the box size arbitrary i used x and y axis as present in popc but in
>> z
>> axis used 10.00000 so there is overlapping of protein and lipid  i think
>> this can create problem
>>
>
> I don't understand if there is a question or problem here.  If something
> is wrong, provide the exact command(s) used and provide images of the
> undesirable output.  Without that information, there's nothing that I or
> anyone else can do to help you.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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